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Prior-Knowledge Description Expectation Prediction Conclusion Leaf Statistics
Evidence_82135 GenProp0125 GENPROP True - {{t}} True - {{t}} Confirmed presence
Evidence_2246 TIGR00036 HMM True - {{∅},{t}} True - {{t}} Confirmed presence
Component_60599 Source of aspartate-semialdehyde None - {{∅}} True - {{t}} Unconfirmed presence
GenProp0193 lysine biosynthesis via alpha-aminoadipate (AAA pathway)~Lysine biosynthesis in fungi has been characterized and begins with the condensation of 2-oxoglutarate and acetyl-CoA to homocitrate and continues through the distinctive intermediate, alpha-aminoadipate. This pathway is distinct in every respect from the diaminopimelate pathway commonly found in bacteria and animals. Recently, an alpha-aminoadipate pathway closely related to the fungal version has been characterized in Thermus thermophilus [1] and appears to be widely distributed among the archaea. None - {{∅}} None - {{∅},{t}} Unexplained
Component_42738 homoaconitate hydratase, LysU subunit None - {{∅}} None - {{∅}} Unexplained
Evidence_55126 TIGR00761 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_2247 TIGR00965 HMM None - {{∅}} None - {{∅}} Unexplained
Component_60594 dihydrodipicolinate reductase None - {{∅}} True - {{t}} Unconfirmed presence
Component_60600 Source of aspartate-semialdehyde True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_82132 TIGR00674 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_55128 TIGR02087 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_82151 TIGR03540 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_82146 TIGR03535 HMM None - {{∅}} None - {{∅}} Unexplained
Component_42742 epsilon-dehydrogenase (proposed) None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_82150 TIGR03539 HMM None - {{∅}} None - {{∅}} Unexplained
Component_60591 succinyl-diaminopimelate transaminase None - {{∅}} None - {{∅}} Unexplained
Evidence_82147 TIGR03536 HMM None - {{∅}} None - {{∅}} Unexplained
Component_42744 acylase None - {{∅}} None - {{∅}} Unexplained
Component_265 dihydrodipicolinate synthase True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_2245 TIGR00674 HMM True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_2249 TIGR01246 HMM None - {{∅}} None - {{∅}} Unexplained
Component_60595 diaminopimelate decarboxylase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_2250 TIGR01900 HMM None - {{∅}} None - {{∅}} Unexplained
Component_60592 diaminopimelate dehydrogenase None - {{∅}} None - {{∅}} Unexplained
Component_60587 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase None - {{∅}} None - {{∅}} Unexplained
Evidence_82138 GenProp0160 GENPROP None - {{∅}} True - {{t}} Unconfirmed presence
Component_42736 homocitrate synthase None - {{∅}} None - {{∅}} Unexplained
Evidence_82139 GenProp0160 GENPROP True - {{∅},{t}} True - {{t}} Confirmed presence
Component_35603 aspartate-semialdehyde dehydrogenase True - {{t}} True - {{t}} Confirmed presence
Component_270 diaminopimelate epimerase True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_47945 TIGR00656 HMM True - {{t}} True - {{t}} Confirmed presence
Component_35602 aspartate kinase True - {{t}} True - {{t}} Confirmed presence
Evidence_82152 TIGR03542 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_55118 TIGR02144 HMM None - {{∅}} None - {{∅}} Unexplained
Component_60596 lysine biosynthesis pathways True - {{t}} True - {{t}} Confirmed presence
Evidence_82140 GenProp0787 GENPROP None - {{∅}} None - {{∅}} Unexplained
GenProp0786 lysine biosynthesis via diaminopimelate (DAP), succinylated branch~ None - {{∅}} None - {{∅}} Unexplained
Evidence_47949 TIGR01745 HMM None - {{∅}} None - {{∅}} Unexplained
GenProp0199 lysine biosynthesis~The basic amino acid lysine may be synthesized by one of two types of pathways pathways in prokaryotes, the diaminopimelate (DAP) pathways and the alpha-aminoadipate (AAA) pathway. The DAP pathway has several variants including the dehydrogenase (reductive) pathway which requires ammonia and NADPH and the acetylated and succinylated pathways which do not. A non-reductive pathway which uses neither acetate or succinate protecting groups is found in plants but has not been observed in prokaryotes. The AAA pathway has a variant found in fungi and plants which has not been observed in prokaryotes. True - {{t}} True - {{t}} Confirmed presence
Component_271 diaminopimelate decarboxylase True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_2252 TIGR01048 HMM True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_47948 TIGR01296 HMM True - {{t}} True - {{t}} Confirmed presence
Evidence_82136 GenProp0193 GENPROP None - {{∅}} None - {{∅},{t}} Unexplained
Evidence_82134 TIGR01048 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_267 aminotransferase pathways None - {{∅}} None - {{∅}} Unexplained
Evidence_55119 TIGR01850 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_55124 TIGR00707 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_55127 TIGR02083 HMM None - {{∅}} None - {{∅}} Unexplained
Component_42737 homoaconitate hydratase, LysT subunit None - {{∅}} None - {{∅}} Unexplained
Component_60588 succinyl-diaminopimelate desuccinylase (DapE) None - {{∅}} None - {{∅}} Unexplained
Component_42743 aminotransferase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_47946 TIGR00657 HMM True - {{t}} True - {{t}} Confirmed presence
GenProp0125 lysine biosynthesis via diaminopimelate (DAP)~The basic amino acid lysine is synthesized in most bacteria and plants via a nine step pathway from aspartate (via aspartate semialdehyde which is also used in a number of other pathways). Most species utilize succinate (from succinyl-CoA) to make an important amide linkage in the ring-opening of piperidine dicarboxylate. The succinate is then hydrolyzed several steps later. Other species carry out analogous transformations with acetate (from acetyl-CoA). Chlamydia and cyanobacteria have been shown to utilize a direct aminotransferase path without the acylation/deacylation steps, and a number of other species apparently also use this variant. Each of these variants are included within this property. A closely related variant (GenProp0788) utilizes the NADPH-dependent enzyme diaminopimelate dehydrogenase (ddh) which incorporates ammonia directly and creates the meso-isomer of diaminopimelate, bypassing the need for the epimerase, DapE. A completely different pathway via alpha-amino adipate exists in fungi and certain bacteria (GenProp0193). Certain obligate intracellular organisms such as Coxiella, Rickettsia and Wolbachia contain all but the final step of this pathway (diaminopimelate decarboxylase). Presumably these organisms have no need of lysine biosynthesis, being able to obtain it from their hosts. The products of the penultimate two steps, however, (LL- and meso-diaminopimelate) are required components of the bacterial cell wall and so the rest of the pathway persists. The formal possibility that the decarboxylase exists in these organsims but is undetected requires that the state of this property remain 'some evidence' as opposed to 'NO'. True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_55120 TIGR02146 HMM None - {{∅}} None - {{∅}} Unexplained
Component_42741 epsilon-carboxykinase (proposed) None - {{∅}} True - {{t}} Unconfirmed presence
GenProp0788 lysine biosynthesis via diaminopimelate (DAP) utilizing ammonia and NADPH~This pathway for the biosynthesis of L-lysine differs from the more common diaminopimelate pathway by the action of diaminopimelate dehydrogenase (ddh). This enzyme requires both ammonia as a nitrogen source (instead of an amino acid via a transaminase) and reductive power in the form of NADPH. Additionally, this pathway does not require the acetyl/succinyl protecting group transformations found in the standard pathway, nor does it require the action of diaminopimelate epimerase. This enzyme has been best characterized in Corynebacterium glutamicum and Bacillus sphaericus. One should note that the ddh enzyme is shown acting on the compound L-2-amino-6-oxoheptanedioate in EC and KEGG representations. This is merely the ring-opened form of 2,3,4,5-tetrahydropicolinate with which it is in equilibrium, and upon which the acyltransferases of the common pathway act. None - {{∅}} None - {{∅},{t}} Unexplained
Evidence_82141 GenProp0786 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_42740 alpha-aminoadipate acylase (proposed) None - {{∅}} None - {{∅}} Unexplained
Evidence_55084 TIGR02130 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_82137 GenProp0788 GENPROP None - {{∅}} None - {{∅},{t}} Unexplained
Component_60593 dihydrodipicolinate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_55129 TIGR01343 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_82149 TIGR03538 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_82148 TIGR03537 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_82131 TIGR01921 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_2251 TIGR00652 HMM True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_55117 TIGR02090 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_55116 TIGR00977 HMM None - {{∅}} None - {{∅}} Unexplained
Component_266 dihydrodipicolinate reductase True - {{∅},{t}} True - {{t}} Confirmed presence
Evidence_82133 TIGR00036 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_47951 TIGR02078 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_55125 TIGR01902 HMM None - {{∅}} None - {{∅}} Unexplained
GenProp0160 aspartate semialdehyde biosynthesis from aspartate~The aspartate semialdehyde biosynthesis is a two step pathway. [2] The product of this pathway can be used in the lysine biosynthesis or in the pathway leading to homoserine involved in the threonine, isoleucine and methionine biosynthesis. There are three different isozymes differed in their sensitivity to regulation by Lys, Met and Thr in Escherichia coli. [1] True - {{t}} True - {{t}} Confirmed presence
Evidence_47947 TIGR00978 HMM None - {{∅}} None - {{∅}} Unexplained